Actually the choice is correct the text after you choose is reversed. I thought the same thing you did and ended up with the clone instead of the original like I wanted.
I put that in in an edit.
Basically, I chose original, then got the line about giving the original away so I quit out before the scene was over and chose 'keep the clone' instead, got the line from lex about keeping the original and I assumed that it was the options that were reversed and I'd end up with the original.
Instead i get a scene about the clone waking up in her bed and being convinced that she got sick an lex saved her. It's clearly the clone because she's suffering from the same muscle problems that all the other clones had.
So then I loaded up an older save and did the opposite (Choose 'keep the clone', get the line from lex about keeping the original. This time assuming that it was the scene after the choice that is reversed, and the choice itself carries over.
Except when I went to visit her in her room a day later, I got exactly the same scene about her being sick.
Near as I can tell, your choice doesn't actually effect anything. There's no scene where you hand her over to Savage and whether you choose to keep the old one or the new one, she ends up weak and shaky from being newly out of the pod anyway.
I guess there aren't any alternative scenes for keeping the original.
All the dev added, as far as I can tell, was a button-option saying 'keep clone/keep original' which triggers a scene of lex talking to himself about why he chose what he chose, with no actual change to the following scenes with Audrey.
And they didn't even do that right.